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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 34156

FusionGeneSummary for SLC22A4_PDLIM4

check button Fusion gene summary
Fusion gene informationFusion gene name: SLC22A4_PDLIM4
Fusion gene ID: 34156
HgeneTgene
Gene symbol

SLC22A4

PDLIM4

Gene ID

6583

8572

Gene namesolute carrier family 22 member 4PDZ and LIM domain 4
SynonymsDFNB60|OCTN1RIL
Cytomap

5q31.1

5q31.1

Type of geneprotein-codingprotein-coding
Descriptionsolute carrier family 22 member 4ET transporterdeafness, autosomal recessive 60ergothioneine transporterintegral membrane transport proteinorganic cation/carnitine transporter 1solute carrier family 22 (organic cation/ergothioneine transporter), memPDZ and LIM domain protein 4LIM domain proteinLIM protein RILenigma homologreversion-induced LIM protein
Modification date2018052220180519
UniProtAcc

Q9H015

P50479

Ensembl transtripts involved in fusion geneENST00000200652, ENST00000491257, 
ENST00000253754, ENST00000379018, 
ENST00000484620, 
Fusion gene scores* DoF score1 X 1 X 1=13 X 1 X 3=9
# samples 13
** MAII scorelog2(1/1*10)=3.32192809488736log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SLC22A4 [Title/Abstract] AND PDLIM4 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, in-frame but not retained their domain.
Tumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSLC22A4

GO:0015697

quaternary ammonium group transport

9426230

HgeneSLC22A4

GO:0015879

carnitine transport

16729965

TgenePDLIM4

GO:0031532

actin cytoskeleton reorganization

21636573


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVKIRPTCGA-BQ-5891-01ASLC22A4chr5

131630702

+PDLIM4chr5

131598302

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
In-frameENST00000200652ENST00000253754SLC22A4chr5

131630702

+PDLIM4chr5

131598302

+
In-frameENST00000200652ENST00000379018SLC22A4chr5

131630702

+PDLIM4chr5

131598302

+
5CDS-intronENST00000200652ENST00000484620SLC22A4chr5

131630702

+PDLIM4chr5

131598302

+
intron-3CDSENST00000491257ENST00000253754SLC22A4chr5

131630702

+PDLIM4chr5

131598302

+
intron-3CDSENST00000491257ENST00000379018SLC22A4chr5

131630702

+PDLIM4chr5

131598302

+
intron-intronENST00000491257ENST00000484620SLC22A4chr5

131630702

+PDLIM4chr5

131598302

+

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FusionProtFeatures for SLC22A4_PDLIM4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SLC22A4

Q9H015

PDLIM4

P50479

Sodium-ion dependent, low affinity carnitinetransporter. Probably transports one sodium ion with one moleculeof carnitine. Also transports organic cations such astetraethylammonium (TEA) without the involvement of sodium.Relative uptake activity ratio of carnitine to TEA is 1.78. A keysubstrate of this transporter seems to be ergothioneine (ET).{ECO:0000269|PubMed:10215651, ECO:0000269|PubMed:15795384}. Isoform 1: Suppresses SRC activation by recognizing andbinding to active SRC and facilitating PTPN13-mediateddephosphorylation of SRC 'Tyr-419' leading to its inactivation.Inactivated SRC dissociates from this protein allowing theinitiation of a new SRC inactivation cycle (PubMed:19307596).Involved in reorganization of the actin cytoskeleton(PubMed:21636573). In nonmuscle cells, binds to ACTN1 (alpha-actinin-1), increases the affinity of ACTN1 to F-actin(filamentous actin), and promotes formation of actin stressfibers. Involved in regulation of the synaptic AMPA receptortransport in dendritic spines of hippocampal pyramidal neuronsdirecting the receptors toward an insertion at the postsynapticmembrane. Links endosomal surface-internalized GRIA1-containingAMPA receptors to the alpha-actinin/actin cytoskeleton. IncreasesAMPA receptor-mediated excitatory postsynaptic currents in neurons(By similarity). {ECO:0000250|UniProtKB:P36202,ECO:0000269|PubMed:19307596, ECO:0000269|PubMed:21636573}. Isoform 2: Involved in reorganization of the actincytoskeleton and in regulation of cell migration. In response tooxidative stress, binds to NQO1, which stabilizes it and protectsit from ubiquitin-independent degradation by the core 20Sproteasome. Stabilized protein is able to heterodimerize withisoform 1 changing the subcellular location of it fromcytoskeleton and nuclei to cytosol, leading to loss of isoforms 1ability to induce formation of actin stress fibers. Counteractsthe effects produced by isoform 1 on organization of actincytoskeleton and cell motility to fine-tune actin cytoskeletonrearrangement and to attenuate cell migration.{ECO:0000269|PubMed:21636573}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+1101_20131552Topological domainCytoplasmic
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+11021_41131552TransmembraneHelical%3B Name%3D1
TgenePDLIM4chr5:131630702chr5:131598302ENST00000253754+07253_31231331DomainLIM zinc-binding
TgenePDLIM4chr5:131630702chr5:131598302ENST00000379018+06253_31231247DomainLIM zinc-binding

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>>>>>>>>>>>>>>>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110218_225131552Nucleotide bindingATP
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110163_171131552Topological domainCytoplasmic
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110193_197131552Topological domainExtracellular
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110219_232131552Topological domainCytoplasmic
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110254_257131552Topological domainExtracellular
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110279_337131552Topological domainCytoplasmic
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110359_371131552Topological domainExtracellular
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110393_399131552Topological domainCytoplasmic
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110421_426131552Topological domainExtracellular
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+11042_141131552Topological domainExtracellular
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110448_460131552Topological domainCytoplasmic
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110482_486131552Topological domainExtracellular
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110508_551131552Topological domainCytoplasmic
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110142_162131552TransmembraneHelical%3B Name%3D2
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110172_192131552TransmembraneHelical%3B Name%3D3
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110198_218131552TransmembraneHelical%3B Name%3D4
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110233_253131552TransmembraneHelical%3B Name%3D5
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110258_278131552TransmembraneHelical%3B Name%3D6
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110338_358131552TransmembraneHelical%3B Name%3D7
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110372_392131552TransmembraneHelical%3B Name%3D8
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110400_420131552TransmembraneHelical%3B Name%3D9
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110427_447131552TransmembraneHelical%3B Name%3D10
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110461_481131552TransmembraneHelical%3B Name%3D11
HgeneSLC22A4chr5:131630702chr5:131598302ENST00000200652+110487_507131552TransmembraneHelical%3B Name%3D12
TgenePDLIM4chr5:131630702chr5:131598302ENST00000253754+071_8431331DomainPDZ
TgenePDLIM4chr5:131630702chr5:131598302ENST00000379018+061_8431247DomainPDZ


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FusionGeneSequence for SLC22A4_PDLIM4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for SLC22A4_PDLIM4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
SLC22A4PDZK1PDLIM4RBPMS, ZNF408, EWSR1, KIR3DL2, G3BP1


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for SLC22A4_PDLIM4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneSLC22A4Q9H015DB00583L-CarnitineSolute carrier family 22 member 4small moleculeapproved|investigational

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RelatedDiseases for SLC22A4_PDLIM4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSLC22A4C0010246Coxsackievirus Infections1CTD_human
HgeneSLC22A4C0014378Enterovirus Infections1CTD_human
HgeneSLC22A4C0027059Myocarditis1CTD_human
TgenePDLIM4C0032460Polycystic Ovary Syndrome1CTD_human